An investigation was conducted on the phytoplankton community structure in the Lake Changshou in March, 2013 to February, 2014 to analyze the seasonal variation of phytoplankton composition density and diversity indices. Differences in the phytoplankton composition among seasons were tested using the Non-metric Multidimensional Scaling and Analysis of Similarities, and environmental influencing factors of phytoplankton composition were identified using Canonical Correspondence Analysis. The results showed that Limnothrix sp., Raphidiopsis sp., Stephanodiscus hantzschii, Komma caudate, Lyngbya sp. and Cryptomonas marssonii were the dominant species, and phytoplankton assemblages were significantly different among seasons. The phytoplankton community was the simplest in spring, and then in summer.The most complicated community occurred in autumn and winter. Canonical correspondence analysis showed that water temperature and nutrients were the most important environmental factors affecting the phytoplankton community structure.Irradiance, permanganate index, oxidation-reduction potential, and dissolved organic carbon also were the key environmental factors affecting the phytoplankton community structure in autumn and winter.